I'm pretty sure that he did lose the powers originally acquired in season 1. I know I read/heard it in an interview somewhere.
With the exception of telekenesis of course, I think they said he had like an "emotional connection" to that power or something and that acquiring it shaped who he is or something like that.
He really doesn't have many powers these days, just super awesome ones.
As of last observation, he's got telekenesis, electrical manipulation, alchemy, the one with touching objects and knowing their history that I forget the name of, and shapeshifting.
As for the whole random disappearing from the car thing, I don't think it's brant to be significant, probably just for dramatic effect and to demonstrate how powerful he is.
To clarify:
For Telekinesis, Sylar had a great amount of guilt over killing Brian Davis for his ability, that is why he retained the ability. It's the emotional connection between Sylar and Davis.
I don't remember Sylar acting guilty, I remember him showing up at the Suresh apartment after killing Brian Davis saying look at what I can do now!!